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Add Jupyter notebook for control file editor
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@hiromatsui
hiromatsui committed Aug 10, 2023
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2,080 changes: 2,080 additions & 0 deletions src/Jupyter/.ipynb_checkpoints/Calypso_control_editor-checkpoint.ipynb
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2,100 changes: 2,100 additions & 0 deletions src/Jupyter/.ipynb_checkpoints/Calypso_control_glossary-checkpoint.ipynb
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2,080 changes: 2,080 additions & 0 deletions src/Jupyter/Calypso_control_editor.ipynb
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2,100 changes: 2,100 additions & 0 deletions src/Jupyter/Calypso_control_glossary.ipynb
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380 changes: 380 additions & 0 deletions src/Jupyter/Test/control_MHD
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begin MHD_control
!!!!! Define for files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! num_subdomain_ctl: number of subdomains
! num_smp_ctl: number of smp processes
!
! mesh_file_head_ctl: header of mesh file (Default: in.domain#)
!
! sph_file_prefix: prefix of spherical transfoem grid
! restart_file_prefix: prefix of restart file
! (Default: restart/rst.step#.domain#)
! field_file_prefix: prefix of snapshot field data
! (Default: out.step#.domain#.udt)
!
! field_file_fmt_ctl: data format for field files
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
begin data_files_def
debug_flag_ctl 'Off'
!
num_subdomain_ctl 4
num_smp_ctl 2
!
restart_file_prefix 'rst_4/rst'
field_file_prefix 'field/out'
restart_file_fmt_ctl 'merged_gz'
field_file_fmt_ctl 'merged_VTK_gz'
end data_files_def
!
!!!!! spatial resolution and parallelization !!!!!!!!!!!!!!!
!
! To Define by external file...
! file spherical_shell_ctl 'file name'
!
! num_domain_ctl: Parallelization information
! num_radial_domain_ctl: Number of radial decompositoin
! num_horizontal_domain_ctl: Number of horizontal decompositoin
!
! truncation_level_ctl: Truncation of spherical harmonics (Lmax)
! ngrid_meridonal_ctl: Number of meridional grid points ( = 1.5 x (Lmax+1))
! num_horizontal_domain_ctl: Number of zonal grid points ( = 3 x (Lmax+1))
!
! radial_grid_type_ctl: Definition for radial grid
! explicit: Set each radial grid explicitly
! Chebyshev: Set Chebyshev collocation points
! equi_distance: Set equi-diatance grid
!
! num_fluid_grid_ctl: Number of radial grids
! fluid_core_size_ctl Size of fluid shell
! ICB_to_CMB_ratio_ctl Aspect ratio (r_o / r_i)
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
file spherical_shell_ctl 'control_resolution'
!
begin model
!!!!! physical values!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! available valuables
! velocity, temperature, pressure, vorticity
! vector_potential, magnetic_field, current_density, magnetic_potential
! composition, perturbation_temp
!
! buoyancy_flux, Lorentz_work, mag_tension_work
! magnetic_ene_generation
! temp_generation, part_temp_gen
! vis_ene_diffuse, mag_ene_diffuse
!
! thermal_diffusion, viscous_diffusion, magnetic_diffusion
! Coriolis_force, buoyancy
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
begin phys_values_ctl
array nod_value_ctl
nod_value_ctl velocity Viz_On Monitor_On
nod_value_ctl temperature Viz_On Monitor_On
nod_value_ctl pressure Viz_On Monitor_On
nod_value_ctl vorticity Viz_On Monitor_On
nod_value_ctl magnetic_field Viz_On Monitor_On
nod_value_ctl current_density Viz_On Monitor_On
!
nod_value_ctl Lorentz_work Viz_On Monitor_On
nod_value_ctl buoyancy_flux Viz_On Monitor_On
!
nod_value_ctl Coriolis_force Viz_On Monitor_On
nod_value_ctl Lorentz_force Viz_On Monitor_On
nod_value_ctl inertia Viz_On Monitor_On
!
nod_value_ctl rot_Coriolis_force Viz_On Monitor_Off
nod_value_ctl rot_Lorentz_force Viz_On Monitor_Off
nod_value_ctl rot_inertia Viz_On Monitor_Off
nod_value_ctl rot_buoyancy Viz_On Monitor_Off
end array nod_value_ctl
end phys_values_ctl
!
!!!!! physical values for time evolution !!!!!!!!!!!!!!!!!!
! aviable valuables: velocity, temperature, magnetic_field
! vector_potential, composition
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
begin time_evolution_ctl
array time_evo_ctl
time_evo_ctl temperature
time_evo_ctl velocity
time_evo_ctl magnetic_field
end array time_evo_ctl
end time_evolution_ctl
!
!!!!! setting for boundary condition
!
begin boundary_condition
array bc_temperature
bc_temperature fixed ICB 1.000
bc_temperature fixed CMB 0.000
end array bc_temperature
!
array bc_velocity
bc_velocity rot_inner_core ICB 0.000
bc_velocity non_slip_sph CMB 0.000
end array bc_velocity
!
array bc_magnetic_field
bc_magnetic_field sph_to_center to_Center 0.000 end
bc_magnetic_field insulator CMB 0.000 end
end array bc_magnetic_field
end boundary_condition
!
!!!!! define of forces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! available forces
! gravity, Coriolis, Lorentz
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
begin forces_define
array force_ctl
force_ctl gravity
force_ctl Coriolis
force_ctl Lorentz
end array force_ctl
end forces_define
!
!!!!! dimensionless numbers !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! available numbers
! Prandtl_number, magnetic_Prandtl_number
! Rayleigh_number, modified_Rayleigh_number
! Reynords_number
! Taylor_number, Ekman_number
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
begin dimensionless_ctl
array dimless_ctl
dimless_ctl Prandtl_number 1.0e-0
dimless_ctl modified_Rayleigh_number 1.1E+2
dimless_ctl Ekman_number 1.0e-3
dimless_ctl magnetic_Prandtl_number 5.0e+0
end array dimless_ctl
end dimensionless_ctl
!
!!!!! Normalization settings !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! define
! coef_4_termal_ctl: time integration and advection of temp
! coef_4_velocity_ctl: time integration and advection of temperature
! coef_4_magnetic_ctl: time integration and advection of magnetic f.
! coef_4_t_diffuse_ctl: coefficients for thermal diffusion
! coef_4_v_diffuse_ctl: coefficients for viscous diffusion
! coef_4_m_diffuse_ctl: coefficients for magnetic diffusion
! coef_4_buoyancy_ctl: coefficients for buoyancy
! coef_4_Coriolis_ctl: coefficients for Coriolis force
! coef_4_Lorentz_ctl: coefficients for Lorantz force
! coef_4_composit_buoyancy_ctl:
! coefficients for compositional buoyancy
! coef_4_induction_ctl: coefficients for magnetic induction
!
! One: 1, Zero (Ignore), Two: 2, Radial_parameter: (1-ri/ro)
! Radial_35: (1-0.35)
!
! Real number.... Power of each numbers
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
begin coefficients_ctl
begin thermal
array coef_4_termal_ctl
coef_4_termal_ctl One 1.0
end array coef_4_termal_ctl
!
array coef_4_t_diffuse_ctl
coef_4_t_diffuse_ctl Prandtl_number -1.0
end array coef_4_t_diffuse_ctl
end thermal
!
!
begin momentum
array coef_4_velocity_ctl
coef_4_velocity_ctl One 1.0
end array coef_4_velocity_ctl
!
array coef_4_press_ctl
coef_4_press_ctl Ekman_number -1.0
end array coef_4_press_ctl
!
array coef_4_v_diffuse_ctl
coef_4_v_diffuse_ctl One 1.0
end array coef_4_v_diffuse_ctl
!
array coef_4_buoyancy_ctl
coef_4_buoyancy_ctl Radial_35 1.0
coef_4_buoyancy_ctl modified_Rayleigh_number 1.0
coef_4_buoyancy_ctl Ekman_number -1.0
end array coef_4_buoyancy_ctl
!
array coef_4_Coriolis_ctl
coef_4_Coriolis_ctl Two 1.0
coef_4_Coriolis_ctl Ekman_number -1.0
end array coef_4_Coriolis_ctl
!
array coef_4_Lorentz_ctl
coef_4_Lorentz_ctl magnetic_Prandtl_number -1.0
coef_4_Lorentz_ctl Ekman_number -1.0
end array coef_4_Lorentz_ctl
end momentum
!
!
begin induction
array coef_4_magnetic_ctl
coef_4_magnetic_ctl One 1.0
end array coef_4_magnetic_ctl
!
array coef_4_m_diffuse_ctl
coef_4_m_diffuse_ctl magnetic_Prandtl_number -1.0
end array coef_4_m_diffuse_ctl
!
array coef_4_induction_ctl
coef_4_induction_ctl One -1.0
end array coef_4_induction_ctl
end induction
end coefficients_ctl
!
!!!!!!!!! model for hydrostatic !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! ref_temperature_ctl: none (No reference of temperature)
! spherical_shell ( for spherical shell model)
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
begin temperature_define
! ref_temp_ctl none
ref_temp_ctl spherical_shell
begin low_temp_ctl
depth 1.5384615384615384
temperature 0.0d0
end low_temp_ctl
begin high_temp_ctl
depth 0.5384615384615384
temperature 1.0d0
end high_temp_ctl
end temperature_define
end model
!
!
!
begin control
!!!!! information for sime integration
begin time_step_ctl
elapsed_time_ctl 80000.
i_step_init_ctl 0
i_step_finish_ctl 120000
!
i_step_check_ctl 100
i_step_rst_ctl 20000
i_step_field_ctl 4000
i_step_sectioning_ctl 500
!
dt_ctl 5.0e-5
time_init_ctl 0.0e-8
end time_step_ctl
!
!!!!! control for restart data
begin restart_file_ctl
rst_ctl dynamo_benchmark_2
! rst_ctl start_from_rst_file
end restart_file_ctl
!
!!!!!! method for time evolution
!
begin time_loop_ctl
scheme_ctl Crank_Nicolson
coef_imp_v_ctl 6.0e-1
coef_imp_t_ctl 6.0e-1
coef_imp_b_ctl 6.0e-1
coef_imp_d_ctl 6.0e-1
end time_loop_ctl
end control
!
begin sph_monitor_ctl
volume_average_prefix 'monitor/sph_ave_volume'
volume_pwr_spectr_prefix 'monitor/sph_pwr_volume'
volume_pwr_spectr_format 'gzip'
!
nusselt_number_prefix 'Nusselt'
nusselt_number_format 'gzip'
!
array volume_spectrum_ctl
begin volume_spectrum_ctl
volume_average_prefix 'monitor/sph_ave_convective'
volume_pwr_spectr_prefix 'monitor/sph_pwr_convective'
volume_pwr_spectr_format 'gzip'
!
inner_radius_ctl 0.588461538461538
outer_radius_ctl 1.488461538461538
end volume_spectrum_ctl
begin volume_spectrum_ctl
volume_average_prefix 'monitor/sph_ave_inner_core'
volume_pwr_spectr_prefix 'monitor/sph_ave_inner_core'
volume_pwr_spectr_format 'ASCII'
!
inner_radius_ctl 0.0
outer_radius_ctl 0.538461538461538
end volume_spectrum_ctl
end array volume_spectrum_ctl
!
begin layered_spectrum_ctl
layered_pwr_spectr_prefix 'monitor/sph_pwr_layer'
layered_pwr_spectr_format 'gzip'
!
array spectr_radius_ctl
spectr_radius_ctl 0.538461538461538
spectr_radius_ctl 0.838461538461538
spectr_radius_ctl 1.238461538461538
spectr_radius_ctl 1.538461538461538
end array spectr_radius_ctl
end layered_spectrum_ctl
!
begin pickup_spectr_ctl
picked_sph_prefix 'monitor/picked_mode'
picked_sph_format 'gzip'
!
array pick_radius_ctl
pick_radius_ctl 0.538461538461538
pick_radius_ctl 1.038461538461538
pick_radius_ctl 1.538461538461538
end array pick_radius_ctl
!
array pick_sph_spectr_ctl
pick_sph_spectr_ctl 1 0
pick_sph_spectr_ctl 2 0
end array pick_sph_spectr_ctl
end pickup_spectr_ctl
!
begin gauss_coefficient_ctl
gauss_coefs_prefix 'monitor/gauss_coefs'
gauss_coefs_format 'gzip'
gauss_coefs_radius_ctl 2.91
!
array pick_gauss_coef_degree_ctl
pick_gauss_coef_degree_ctl 1
end array pick_gauss_coef_degree_ctl
end gauss_coefficient_ctl
!
begin dynamo_benchmark_data_ctl
dynamo_benchmark_file_prefix 'monitor/dynamobench'
dynamo_benchmark_file_format 'gzip'
nphi_mid_eq_ctl 512
end dynamo_benchmark_data_ctl
end sph_monitor_ctl
!
begin visual_control
array cross_section_ctl
file cross_section_ctl control_psf_CMB
file cross_section_ctl control_psf_ICB
file cross_section_ctl control_psf_eq
file cross_section_ctl control_psf_z0.3
file cross_section_ctl control_psf_s0.55
end array cross_section_ctl
!
array isosurface_ctl
file isosurface_ctl control_iso_temp
end array isosurface_ctl
end visual_control
!
begin dynamo vizs control
file zonal mean section ctl control_psf_zm
end dynamo vizs control
end MHD_control
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